The protest took place when the Pakistani cricketer- turned-politician along with his new wife Reham Khan arrived at the Army Public School to meet the students.
The parents of deceased students who lost their children in the school tragedy chanted "Go Imran Go" while holding placards rejecting Khan's visit.
The attack claimed lives of 150 people, including 134 children, who were butchered by Taliban militants. The school reopened on Monday after remaining closed for weeks.